The traditional concept of "tonic food" and demand for traditional Chinese medicine make pangolins the largest population of illegally smuggled mammals in the world. Illegal hunting and trade are not only responsible for the sharp decline in pangolin populations but also provide conditions for pathogenic transmission. In 2021, we rescued 21 confiscated unhealthy Malayan pangolins, none of which survived. This study aimed to investigate the reasons for their unexpected deaths and the potential pathogens that may be transmitted during smuggling. Physical examination found that more than 80% pangolins were parasitized with A. javanense ticks. Autopsy and pathological staining analysis revealed multiple organ damage in the deceased pangolins. Pathogens nucleic acid detection of 33 tick samples showed that the positive rate of Rickettsia spp., Anaplasma spp., Ehrlichia spp. Babesia spp., and Colpodella spp. were 90.91%, 6.06%, 6.06%, 15.15% and 18.18%, respectively. Furthermore, pangolin samples were positive for Rickettsia spp. (42.86%, 9/21), Ehrlichia sp. (4.76%, 1/21), and Babesia sp. (4.76%, 1/21). This study confirmed that spotted fever triggered by Rickettsia spp. from A. javanense might accelerate the most death of confiscated pangolins, while Ehrlichia sp., and Babesia sp. infection potentially accelerating a few deaths. Of note, A. javanense ticks carrying Colpodella spp. were detected for the first time in Malayan pangolins. However, whether Colpodella spp. are pathogenic to pangolins is unknown. Further research on the diagnosis, treatment, surveillance, and elimination of ticks and tick-borne diseases in humans, livestock, and wildlife should provide insight into wildlife conservation and zoonotic disease prevention.